The fire service was called out to St John's Hill School on Wednesday after an alarming smell began emanating from a drum near the swimming pool.
The incident happened about 11am on Wednesday.
Three fire trucks and a hazardous materials truck were at the school and two of the responders had to suit up in orange, fully encapsulated outfits for the hazard identification.
Whanganui fire service group manager Aaron Summerhays said the school had to be evacuated, but luckily, the school holiday meant there was only a few staff around.
"It's just been a mismatch of a couple of products around the swimming pool," he said.
"It's an unknown so we've got to treat everything as a worst-case scenario until we know what we're dealing with."
The odour was a lot like chlorine, Summerhays said, and they had to get the hazard identified before it could be properly dealt with.
The hazardous materials workers took advice from the Queensland Poisons Information Centre about how to remove the substance safely, once it had been identified.
Summerhays said there was no reaction to what he called a byproduct of two chemicals that were wrongly mixed together.
"All went quite nicely," he said.
Once the product was removed the responders who dealt to it had to be hosed down for decontamination in the driveway of the school.
No houses around the school had to be evacuated.